Problems with SVG save in illustrator

[SampigeSampie]

Hello everyone willing to help,

I was working on converting a drawing from Kim Jung Gi to an Illustrator file and to colour it in. I am no expert in Illustrator and I think I must have saved the file as a SVG to start with as I can't find a normal Illustrator file (normally it always saves like that automatically). When I opened the save today it had merged all layers into one and grouped every item object and path seperately. I would sometimes turn the opacity of parts i had already coloured in down to 0 so they would't interfere with what I was doing but  now it has glitched and even though the opacity of those objects is on full I can't see the fill. Most of the strokes have also dissapeared but I can still see them if I turn up the thickness. I really don't know what the case is so sorry if my explanation isn't too helpful. I will add the file ( I had to save it as Illustrator EPS file to add it as an attachment or I would get an error) and a picture I saved from the most recent moment everything still worked and was coloured in. 

Thanks in advance and I will try to respond to responses as quick as I can.

Sammy

[Monika Gause]

While you're working ona file, always save it as an AI file.

Neither SVG nor EPS is suitable as a work file.

[SampigeSampie]

Yes I unfortunately did not notice I didn't and found out the hard way. But is there a way to fix this is more interesting to me right now. 

[Monika Gause]

When the layers are gone, then the only thing that could help, would be a backup.

If you don't have a backup, you will need to set up layers again and move the objects into them.

[SampigeSampie]

I can deal with setting the layers up again, the real problem I have that right now is that the some objects won't fill in properly. The objects had a working stroke and fill. Now with some the stroke is gone but if I change it it appears again, the fill still has the colour I picked selected but no matter what I do it won't appear. It'l just look empty with no way I can find of filling the object again. 

[Monika Gause]

I'm sorry I don't understand a word of your problem. I can't see inside your head. And I don't want to guess.

Please post screenshots that show the problems.

Also: please embed screenshots in your post, don't attach them.

[SampigeSampie]

I'm sorry it's my first time posting here I'll remember it, I can't upload screenshots right now unfortunately but I'll try to explain it once more. I had multiple objects that I made with the pen and coloured in, after opening the file later those objects were no longer coloured in. If I click on one of them I can see that the fill colour is still selected, it just won't show up. I can try to change the colours but nothing happens. The opacity is at 100% so that's not the problem. I hope this is more clear and thank you for your help.